How can GPU be used instead of CPU for background processing in a Python script?
Not an answer re using GPU.

Not sure re using GPU, can however suggest 
stripping this back to have only import and export operators and use API methods to add modifiers, create modified mesh, remove modifiers, swap in modified mesh.  

May not speed it up too much, will if looping multiple imported objects.

import bpy
context = bpy.context
# import 
ob = context.object

#add decimate modifer
dm = ob.modifiers.new("decimate", 'DECIMATE')
dm.ratio = 0.03

# Add Laplacial smooth modifier 10 1.0 0"
lsm = ob.modifiers.new("ls", 'LAPLACIANSMOOTH')
lsm.use_y = False
lsm.use_x = False
lsm.lambda_border = 0
lsm.iterations = 10
lsm.lambda_factor = 1.0
# create modified mesh
context.scene.update()
me = ob.to_mesh(context.depsgraph, True)
# remove modifiers
ob.modifiers.clear()
# swap in the mesh
ob.data = me
# export


Note this is for 2.8.  Check the docs for ob.to_mesh(..) in prior versions.

A modified mesh can also be created from object via bmesh module.

If there are materials will need to link those to new mesh too.